Pippin pulse

Manufactured by Sage Science

Sourced in United States

The Pippin Pulse is a lab equipment product designed for nucleic acid electrophoresis. It performs size-based separation and purification of DNA and RNA samples.

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Lab products found in correlation

Nanodrop 2000, by Thermo Fisher Scientific (6 mentions) Qubit fluorometer, by Thermo Fisher Scientific (4 mentions) Seakem gold agarose 1, by Lonza (3 mentions) Qubit 3.0 fluorometer, by Thermo Fisher Scientific (3 mentions) Dsdna broad range assay kit, by Thermo Fisher Scientific (2 mentions) Chef dna size standard ladder, by Bio-Rad (2 mentions) Quick load 1 kb extend dna ladder, by Bio-Rad (2 mentions) Nugenius imaging system, by Syngene (2 mentions) Femto pulse system, by Agilent Technologies (1 mentions) Saphyr instrument, by Bionano Genomics (1 mentions) Saphyr chip, by Bionano Genomics (1 mentions) Qubit dsdna br assay kit, by Thermo Fisher Scientific (1 mentions) Femto pulse instrument, by Agilent Technologies (1 mentions) Prep blood and cell culture dna isolation kit, by Bionano Genomics (1 mentions) Tissueruptor, by Qiagen (1 mentions) Qubit dna br assay kit, by Thermo Fisher Scientific (1 mentions) Genomic dna 165 kb kit, by Agilent Technologies (1 mentions)

6 protocols using pippin pulse

Comprehensive DNA Quantification and Quality Assessment

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DNA was quantified using a Qubit fluorometer with the dsDNA Broad Range Assay kit (Thermo Fisher Scientific) following the manufacturer’s instructions. DNA purity was evaluated using Nanodrop 2000 (Thermo Fisher Scientific) UV/Vis measurements. To determine the cell line gDNA integrity pulse-field gel electrophoresis, using the Pippin Pulse (Sage Science) was performed. For this analysis a SeaKem® GOLD Agarose 1% (Lonza) gel was prepared in 0.5× TBE buffer (Thermo Fisher Scientific). Approximately 150 ng of DNA sample was loaded together with CHEF DNA Size Standard Ladder (BIO-RAD) and Quick-Load 1 kb Extend DNA Ladder (NEB) to aid size determination. Fragments were separated using a pre-set 5–80 kb protocol. After the run, the gel was visualised using a NuGenius imaging system (Syngene). DNA integrity of the clinical samples was assessed with the Femto Pulse System using the Genomic DNA 165 kb Kit (Agilent Technologies) following the manufacturer’s protocol. The gDNA samples were stored at 4 °C.

Keraite I., Becker P., Canevazzi D., Frias-López C., Dabad M., Tonda-Hernandez R., Paramonov I., Ingham M.J., Brun-Heath I., Leno J., Abulí A., Garcia-Arumí E., Heath S.C., Gut M, & Gut I.G. (2022). A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome. Nature Communications, 13, 5902.

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High-Molecular DNA Labeling and Imaging

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DNA was quantified using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific, USA). The integrity of high‐molecular weight DNA was determined by pulse‐field gel electrophoresis (Pippin Pulse, Sage Science). Samples with > 150kb molecular weight at the concentration of 45‐200 ng/μl were used for labeling experiments. DNA labeling was carried out according to Bionano PrepTM Labeling ‐ NLRS Protocol (Bionano Genomics #U30024), and consisted of four consecutive steps (Nick, Label, Repair and Stain). First, 300 ng of high molecular weight DNA was nicked using endonuclease Nb.BssSI in 10×Buffer 3.1 (Bionano Genomics, USA) for 2 h at 37oC. Second, 1.5 μl of 10×Labeling Mix (Bionano Genomics) and 1.0 μl Taq DNA Polymerase (Bionano Genomics) was added and the sample left to stand for 1 h at 72oC. Third, labeled DNA was repaired using 5 μl Repair Master Mix for 30 min at 37oC. Forth, DNA was stained overnight using 41.8 μl of Staining Master Mix (Bionano Genomics, USA). The stained DNA was quantified as above. DNA was used at 3‐10 ng/μl, loaded into a Saphyr chip (Bionano Genomics, USA), and the fluorescent DNA molecules were imaged using the Saphyr instrument (Bionano Genomics, USA).

Zheng Y., Kong L., Xu H., Lu Y., Zhao X., Yang Y., Yu G., li P., Liang F., Jin H, & Kong X. (2019). Rapid prenatal diagnosis of Facioscapulohumeral Muscular Dystrophy 1 by combined Bionano optical mapping and karyomapping. Prenatal Diagnosis, 40(3), 317-323.

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Isolating Fungal Genomic DNA from Sporocarps

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Two sporocarps, which were probably ramets derived from a single shiro (radius > 2 m) that has been generating sporocarps for more than 20 years,¹⁰ were collected from Ina, Nagano, Japan. The sporocarps were flash-frozen in liquid nitrogen, dried under vacuum, and then stored at room temperature until needed for DNA extraction.
Genomic DNA was extracted from the dried stipes using the cetyltrimethylammonium bromide (CTAB) method.¹¹ The concentration of the extracted DNA was measured using the Qubit dsDNA BR assay kit (Thermo Fisher Scientific, Waltham, MA, USA), and DNA fragment length was evaluated by agarose gel electrophoresis with Pippin Pulse (Sage Science, Beverly, MA, USA).

Kurokochi H., Tajima N., Sato M.P., Yoshitake K., Asakawa S., Isobe S, & Shirasawa K. (2023). Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake). DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, 30(3), dsad006.

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Isolation of Ultra-High-Molecular-Weight DNA

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For tissue, HMW DNA was extracted using the Bionano animal tissue DNA isolation fibrous tissue protocol (cat no. RE-013-10; document number 30071), according to the manufacturer’s guidelines. A total of 25–30 mg was fixed in 2% formaldehyde and homogenized using the Qiagen TissueRuptor or manual tissue disruption. For nucleated blood, 27–54 μl was used with an adapted protocol (Bionano, personal communication) of the Bionano Prep Blood and Cell Culture DNA Isolation Kit (cat no. RE-130-10). Lysates were embedded into agarose plugs and treated with Proteinase K and RNase A. Plugs were then purified by drop dialysis with 1× TE. DNA quality was assessed using pulse field gel electrophoresis (PFGE) (Pippin Pulse, SAGE Science, Beverly, MA) or the Femto Pulse instrument (Agilent). PFGE revealed that we isolated ultra-high-molecular-weight DNA between ~100 and ~500 kb long.

Rhie A., McCarthy S.A., Fedrigo O., Damas J., Formenti G., Koren S., Uliano-Silva M., Chow W., Fungtammasan A., Kim J., Lee C., Ko B.J., Chaisson M., Gedman G.L., Cantin L.J., Thibaud-Nissen F., Haggerty L., Bista I., Smith M., Haase B., Mountcastle J., Winkler S., Paez S., Howard J., Vernes S.C., Lama T.M., Grutzner F., Warren W.C., Balakrishnan C.N., Burt D., George J.M., Biegler M.T., Iorns D., Digby A., Eason D., Robertson B., Edwards T., Wilkinson M., Turner G., Meyer A., Kautt A.F., Franchini P., Detrich HW I.I.I., Svardal H., Wagner M., Naylor G.J., Pippel M., Malinsky M., Mooney M., Simbirsky M., Hannigan B.T., Pesout T., Houck M., Misuraca A., Kingan S.B., Hall R., Kronenberg Z., Sović I., Dunn C., Ning Z., Hastie A., Lee J., Selvaraj S., Green R.E., Putnam N.H., Gut I., Ghurye J., Garrison E., Sims Y., Collins J., Pelan S., Torrance J., Tracey A., Wood J., Dagnew R.E., Guan D., London S.E., Clayton D.F., Mello C.V., Friedrich S.R., Lovell P.V., Osipova E., Al-Ajli F.O., Secomandi S., Kim H., Theofanopoulou C., Hiller M., Zhou Y., Harris R.S., Makova K.D., Medvedev P., Hoffman J., Masterson P., Clark K., Martin F., Howe K., Flicek P., Walenz B.P., Kwak W., Clawson H., Diekhans M., Nassar L., Paten B., Kraus R.H., Crawford A.J., Gilbert M.T., Zhang G., Venkatesh B., Murphy R.W., Koepfli K.P., Shapiro B., Johnson W.E., Di Palma F., Marques-Bonet T., Teeling E.C., Warnow T., Graves J.M., Ryder O.A., Haussler D., O’Brien S.J., Korlach J., Lewin H.A., Howe K., Myers E.W., Durbin R., Phillippy A.M, & Jarvis E.D. (2021). Towards complete and error-free genome assemblies of all vertebrate species. Nature, 592(7856), 737-746.

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High-Molecular-Weight gDNA Extraction from Liver

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High-molecular-weight (HMW) gDNA was extracted from frozen liver using the Nanobind tissue kit (Circulomics) following the manufacturer’s protocol. Briefly, two cryopreserved liver aliquots of 38 mg and 24 mg were homogenized under cryogenic conditions on dry ice, using a mortar and pestle. The pulverized tissue was collected into 1.5 ml tubes with lysis buffer (Circulomics). Nanobind disk (Circulomics) was used on fresh supernatant for the gDNA binding. The HMW gDNA eluate was quantified by Qubit DNA BR Assay kit (Thermo Fisher Scientific) and the DNA purity was evaluated using Nanodrop 2000 (Thermo Fisher Scientific) UV/Vis measurements. The gDNA integrity was evaluated with pulsed-field gel electrophoresis SeaKem® GOLD Agarose 1% (Lonza), using the Pippin Pulse (Sage Science). The gDNA samples were stored at 4°C.

Gomez-Garrido J., Cruz F., Alioto T.S., Feiner N., Uller T., Gut M., Sanchez Escudero I., Tavecchia G., Rotger A., Otalora Acevedo K.E, & Baldo L. (2023). Chromosome-level genome assembly of Lilford’s wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain). DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, 30(3), dsad008.

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DNA Quality Control for Cell Lines and Samples

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DNA quality control. DNA was quantified using a Qubit fluorometer with the dsDNA Broad Range Assay kit (Thermo Fisher Scientific) following the manufacturer's instructions. DNA purity was evaluated using Nanodrop 2000 (Thermo Fisher Scientific) UV/Vis measurements. To determine the cell line gDNA integrity pulse-field gel electrophoresis, using the Pippin Pulse (Sage Science) was performed. For this analysis a SeaKem® GOLD Agarose 1% (Lonza) gel was prepared in 0.5× TBE buffer (Thermo Fisher Scientific). Approximately 150 ng of DNA sample was loaded together with CHEF DNA Size Standard Ladder (BIO-RAD) and Quick-Load 1 kb
Extend DNA Ladder (NEB) to aid size determination. Fragments were separated using a pre-set 5-80 kb protocol. After the run, the gel was visualized using a NuGenius imaging system (Syngene). DNA integrity of the clinical samples was assessed with the Femto Pulse System using the Genomic DNA 165 kb Kit (Agilent Technologies) following the manufacturer's protocol. The gDNA samples were stored at 4ºC.

Keraite I., Becker P., Canevazzi D., Frías-López C., Dabad M., Tonda R., Paramonov I., Ingham M., Brun‐Heath I., Leno-Colorado J., Abulí A., Garcia-Arumí E., Heath S., Gut M., & Gut M. (2022). Novel method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome.

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